I have an issue with WGCNA analysis on RNA-seq data. I have an error message when calculating co-expression similarity and adjacency at the stage of network construction and module detection. So when I input the function:

adjacency = adjacency(datExpr, power = softPower)

the following errror appears: Error in cor(datExpr, use = "p") : REAL() can only be applied to a 'numeric', not a 'integer'

The is my first time at using WGCNA, any advice would be appreciated. Thanks in advance. This is the code for R 3.3.2:

library("WGCNA")

options(stringsAsFactors = FALSE)

femData = read.csv("Counts ALL-2-VP.csv")

dim(femData)

names(femData)

datExpr0 = as.data.frame(t(femData[, -c(1:1)]))

names(datExpr0) = femData$EnsemblID

rownames(datExpr0) = names(femData)[-c(1:1)]

View(datExpr0)

View(femData)

gsg = goodSamplesGenes(datExpr0, verbose = 3)

gsg$allOK

if (!gsg$allOK) {if (sum(!gsg$goodGenes)>0) printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", "))); if (sum(!gsg$goodSamples)>0) printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", "))); datExpr0 = datExpr0[gsg$goodSamples, gsg$goodGenes] } sampleTree = hclust(dist(datExpr0), method = "average")

sizeGrWindow(12,9)

par(cex = 0.6)

par(mar = c(0,4,2,0))

plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, cex.axis = 1.5, cex.main = 2)

datExpr = datExpr0

nGenes = ncol(datExpr)

nSamples = nrow(datExpr)

save(datExpr, file = "FemaleLiver-01-dataInput.RData")

lnames = load(file = "FemaleLiver-01-dataInput.RData")

lnames

disableWGCNAThreads()

powers = c(c(1:10), seq(from = 12, to=20, by=2))

sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)

sizeGrWindow(9, 5)

par(mfrow = c(1,2))

cex1 = 0.9

plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence")); text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])sft$fitIndices[,2], labels=powers,cex=cex1,col="red")

abline(h=0.78,col="red")

plot(sft$fitIndices[,1], sft$fitIndices[,5], xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n", main = paste("Mean connectivity")) text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1,col="red")

softPower = 12

adjacency = adjacency(datExpr, power = softPower)

The sessionInfo:

sessionInfo function (package = NULL) { z <- list()

z$R.version <- R.Version()

z$platform <- z$R.version$platform

if (nzchar(.Platform$r_arch)) 

    z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")

z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, 
    "-bit)")

z$locale <- Sys.getlocale()
if (.Platform$OS.type == "windows") {
    z$running <- win.version()
}
else if (nzchar(Sys.which("uname"))) {
    uname <- system("uname -a", intern = TRUE)
    os <- sub(" .*", "", uname)
    z$running <- switch(os, Linux = if (file.exists("/etc/os-release")) {
        tmp <- readLines("/etc/os-release")
        t2 <- if (any(startsWith(tmp, "PRETTY_NAME="))) sub("^PRETTY_NAME=", 
            "", grep("^PRETTY_NAME=", tmp, value = TRUE)[1L]) else if (any(startsWith(tmp, 
            "NAME"))) sub("^NAME=", "", grep("^NAME=", tmp, 
            value = TRUE)[1L]) else "Linux (unknown distro)"
        sub("\"(.*)\"", "\\1", t2)
    } else if (file.exists("/etc/system-release")) {
        readLines("/etc/system-release")
    }, Darwin = {
        ver <- readLines("/System/Library/CoreServices/SystemVersion.plist")
        ind <- grep("ProductUserVisibleVersion", ver)
        ver <- ver[ind + 1L]
        ver <- sub(".*<string>", "", ver)
        ver <- sub("</string>$", "", ver)
        ver1 <- strsplit(ver, ".", fixed = TRUE)[[1L]][2L]
        sprintf("%s %s %s", ifelse(as.numeric(ver1) < 12, 
            "OS X", "macOS"), switch(ver1, `4` = "Tiger", 
            `5` = "Leopard", `6` = "Snow Leopard", `7` = "Lion", 
            `8` = "Mountain Lion", `9` = "Mavericks", `10` = "Yosemite", 
            `11` = "El Capitan", `12` = "Sierra", ""), ver)
    }, SunOS = {
        ver <- system("uname -r", intern = TRUE)
        paste("Solaris", strsplit(ver, ".", fixed = TRUE)[[1L]][2L])
    }, uname)
}
if (is.null(package)) {
    package <- grep("^package:", search(), value = TRUE)
    keep <- vapply(package, function(x) x == "package:base" || 
        !is.null(attr(as.environment(x), "path")), NA)
    package <- .rmpkg(package[keep])
}
pkgDesc <- lapply(package, packageDescription, encoding = NA)
if (length(package) == 0) 
    stop("no valid packages were specified")
basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
    x$Priority == "base")
z$basePkgs <- package[basePkgs]
if (any(!basePkgs)) {
    z$otherPkgs <- pkgDesc[!basePkgs]
    names(z$otherPkgs) <- package[!basePkgs]
}
loadedOnly <- loadedNamespaces()
loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
if (length(loadedOnly)) {
    names(loadedOnly) <- loadedOnly
    pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
    z$loadedOnly <- pkgDesc[loadedOnly]
}
class(z) <- "sessionInfo"
z

} <bytecode: 0x000000001acd2c88=""> <environment: namespace:utils="">